Figure 2-7
A. Oxygen (65% by wt.); Carbon (18.5%); H(9.5%); N (3.3%); Ca (1.5%); P (1.0%)
B. What is special about these? ==> Stability and Versatility in making Covalent Bonds
1. C: At. No. 6 ==> 6 electrons -- 1s2 2s2 2px1 2py1 2pz0 <-- no. of electrons2nd shell has room for 4 more electrons ==> can form 4 chemical bonds by sharing pairs of electrons, 1 electron in each pair from C and 1 from the other atom (more about this later).
2. O: Atomic. No. 8 ==> 8 electrons -- 1s2 2s2 2px2 2py1 2pz1. Room for 2 more ==> 2 bonds
3. H: Atomic. No. 1 ==> 1 electron -- 1s1. Room for 1 electron ==> 1 bond
4. N: Atomic. No. 7 ==> 7 electrons -- 1s2 2s2 2px1 2py1 2pz1 -- room for 3 more electrons ==> 3 bonds.
C. Electronegativity -- the tendency of an atom to attract more than its own complement of electrons. Let's consider 3 situations.
1. Atoms with low electronegativity, C and H: C--C and C--H bonds share bonding electrons equally ==> form strong stable covalent bonds with no polarity (i.e. no partial negative or positive charages at different atoms).2. Atoms with moderate electronegativity, O and N: O--C, O--H, N--C, and N--H bonds have uneven sharing of bonding electrons ==> less stable covalent bonds which are polar; O or N have partial negative charges on them (more than their share of bonding electrons) while H and C have partial positive charges (less than their share).
A. Carbon is very versatile - can form bonds with 4, 3, or 2 different atoms. We will only discuss the first two possibilities.
1. Bonds with 4 different atoms ==> Tetrahedral Configuration: want to form 4 equivalent electron orbitals to make 4 equivalent bonds; combine 2s + 2px + 2py + 2pz atomic orbitals to produce 4 sp3 hybrid atomic orbitals with 1 electron in each. Each of these orbitals should be as far as possible from its neighbors ==> They point to the corners of a tetrahedron, a 3-sided pyramid, with C at the center; the angle between each orbital (bond) is 109°. Bonds are formed when each sp3 hybrid orbital + electron combines with an orbital of another atom which also has 1 electron to form a molecular orbital with a pair of electrons shared by both atoms. This produces a s-bond in which the bonding electrons spend most of their time directly between the two atoms. e.g. CH4.
2. Bonds with 3 other atoms ==> Planar Configuration: want to form 3 equivalent orbitals ==> combine 2s + 2px + 2py to produce 3sp2 hybrid orbitals; these should also be as far from one another as possible ==> they lie on a plane and point to the corners of an equilateral triangle with C at its center and 120° angles between them. These orbitals form s-bonds with the other atoms. The remaining 2pz orbital is perpendicular to the plane of the sp2 orbitals and can form a second bond with one of the 3 atoms; this p-bond has bonding electrons which spend most of their time above or below the plane of the sp2 orbitals.
B. Oxygen and
Nitrogen have similar bonding geometries
1. Nitrogen commonly forms bonds with sp3 hybrid orbitals; in the case of N, however, one of the sp3 orbitals contains a non-bonding pair of electrons associated only with N; this pair of non-bonding electrons can be used to form a bond with a proton (a hydrogen atom with no electrons) to form NH4+, the ammonium ion.2. Oxygen also commonly uses sp3 hybrid orbitals for bonding; however O uses 2 sp3 orbitals to hold non-bonding electron pairs associated only with the O nucleus because O has 2 more electrons than C. For example water, H2O
3. Both O and N are electronegative ==> their bonds with H and C are polar
4. Both O and N can form double bonds similar to those formed by C; sp2 hybrid orbitals are used to form a s bond and the remaining 2pz orbital is used to form a p bond.
5. Both O and N can form an extra bond by using a pair of non-bonding electrons to form a bond to an atom (or molecule) which is missing an electron (usually a proton, H+); the molecule which results will have a positive charge
1. Hydrogen Bonds -- partial negative charges on O's and positive charges on H's cause electrostatic attractions bettween H's and O's. Each H2O can bond to 4 other H2O 's. Gives water:a) high boiling point; b) high surface tension ==> capillary action; c) high heat of vaporization; d) expands upon freezing; e) versatile solvent for polar molecules; f) high specific heat==>stabilizes temperature
Hydrogen Bond: a H is shared unequally by 2 electronegative atoms (generally N or O). The atom most closely associated with the H is the H-Donor atom and the other is the H-Acceptor atom. This is an electrostatic attraction betweenthe atoms, and the H-bond is strongest when the 3 atoms (donor, acceptor, and H) line up. H-bonds hold water molecules together, so it is hard to pull them apart giving water a high boiling point, high heat of vaporization, etc.
2. H2O can dissociate -- H2O == H+ + OH-This reaction is in equilibrium with Keq = 1 x 10-14 at 25°C ==> [H+][OH-] = 1 x 10-14 M2 in pure water [H+] = [OH-] = 1 x 10-7 M
3. Acids and Bases -- some compounds can change [H+] and [OH-] when they are dissolved in water; but [H+].[ OH-] is always constant at a fixed temp.a) acids -- are H+ donors and increase [H+] decreasing [OH-]b) bases -- are H+ acceptors and decrease [H+] increasing [OH-]
4. pH -- organisms are composed mostly of water and contains groups of atoms which can bind or release H+ ==> they are very sensitive to changes of [H+] which range over orders of magnitude (powers of 10). Scientists have developed a scale to measure changes of [H+] by powers of 10. pH = -log10[H+] and varies from 0 - 14. The negative of the logarithm is used so that pH values will be positive numbers. Note that a change in pH by 1 unit represents a change in [H+] by 10x.
1. Alkanes -- hydrocarbons which contain only single bonds (saturated); C--C and C--H.a) methane, CH4; ethane, CH3CH3 ; propane, CH3CH2CH3 ; butane, CH3CH2CH2CH3All of these are gases at room temperature and 1 atmosphere pressure even though the smallest, methane, has about the same size and mass as a water molecule.
b) larger compounds named by number of C atoms: pentane, hexane, heptane, octane (octane long ago determined to be the ideal fuel for automobiles ==> octane ratings of gasolines). Larger alkanes are used as lubricating oils and paraffin (another name for alkanes is paraffins).
c) can have numerous branch points because sp3 orbitals point in 4 different directions ==> infinite variety of possible compounds
d) can also form cyclic structures if head of molecule bonds with tail of molecule, e.g. cyclohexane2. Alkenes -- hydrocarbons which contain one or more double bonds; H2C==CH2 -- ethene
a) less reduced than alkanes, but still react vigorously with oxygenb) more rigid than alkanes because molecule cannot rotate around double bond.
3. Aromatic compounds: These are cyclic structures usually based on benzene which has 6 carbon atoms bonded together forming a hexagon with each C also bonded to a H. the 2pz orbitals of the C's form a special type of bond which makes the ring especially stable and electron rich.
1. Functional Groups -- When other atoms are bonded to hydrocarbons, they confer different properties to the molecule(s) usually reflecting their greater electronegativity which produces polar bonds; these polar bonds make organic compounds less hydrophobic, more hydrophilic, and more reactive. The parts of the organic compound containing these atoms are called Functional Groups. Following are some examples of functional groups; R indicates the remaining part of the molecule which could be a simple hydrocarbon or a complex structure containing other functional groups. See Table 4.3 and Figure belowa) O-containing functional groups (in order of increasing oxidation state): alcohols; carbonyls, aldehydes and ketones; carboxylic acidsb) N-containing: amines
c) S-containing: sulfhydral ==> thiols(similar properties as alcohols)
d) P-containing: organic phosphates (organic acids).
2. Two functional groups can react together to form a new type of functional group; these reactions are very important in the formation of biological moleculesa) esters -- an acidic group (carboxylic acid or organic phosphate) can react with an alcohol (or thiol) to form an ester:b) amides -- an acidic group reacting with an amino group
1. Structural Isomers -- differ in covalent arrangement of atoms
2. Geometric Isomers -- contain the same sequence of covalent bonds, but the groups are arranged differently; e.g. cis and trans isomers about a double bond.
3. Enantiomers -- non-superimposable mirror images. Because of its tetrahedral bonding geometry, a C atom bonded to 4 different atoms or different structural groups can exist in 2 forms which are mirror images of one another and which cannot be superimposed upon one another. This is an important concept in biology because organisms usually contain (use or produce) only one of two possible enantiomers of a compound. Such molecules (and the C atom) are sometimes called chiral after the Greek word for hand; your left and right hands are the most common examples of non-superimposable mirror images.
S-Thalidomide causes serious birth defects when pregnant women take it during their first trimester.
R-Thalidomide does not cause birth defects and has therapeutic uses.
